public class AsaCalculator extends Object
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_N_SPHERE_POINTS |
static int |
DEFAULT_NTHREADS |
static double |
DEFAULT_PROBE_SIZE |
static double |
NUC_CARBON_VDW |
static double |
NUC_NITROGEN_VDW |
static double |
OXIGEN_VDW |
static double |
PHOSPHOROUS_VDW |
static double |
SULFUR_VDW |
static double |
TETRAHEDRAL_CARBON_VDW |
static double |
TETRAHEDRAL_NITROGEN_VDW |
static double |
TRIGONAL_CARBON_VDW |
static double |
TRIGONAL_NITROGEN_VDW |
Constructor and Description |
---|
AsaCalculator(Atom[] atoms,
double probe,
int nSpherePoints,
int nThreads)
Constructs a new AsaCalculator.
|
AsaCalculator(Structure structure,
double probe,
int nSpherePoints,
int nThreads,
boolean hetAtoms)
Constructs a new AsaCalculator.
|
Modifier and Type | Method and Description |
---|---|
double[] |
calculateAsas()
Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
|
GroupAsa[] |
getGroupAsas()
Calculates ASA for all atoms and return them as a GroupAsa
array (one element per residue in structure) containing ASAs per residue
and per atom.
|
static double |
getRadius(Atom atom)
Gets the van der Waals radius of the given atom following the values defined by
Chothia (1976) J.Mol.Biol.105,1-14
NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates"
slightly the heavy atoms to account for Hydrogens.
|
public static final int DEFAULT_N_SPHERE_POINTS
public static final double DEFAULT_PROBE_SIZE
public static final int DEFAULT_NTHREADS
public static final double TRIGONAL_CARBON_VDW
public static final double TETRAHEDRAL_CARBON_VDW
public static final double TRIGONAL_NITROGEN_VDW
public static final double TETRAHEDRAL_NITROGEN_VDW
public static final double SULFUR_VDW
public static final double OXIGEN_VDW
public static final double NUC_CARBON_VDW
public static final double NUC_NITROGEN_VDW
public static final double PHOSPHOROUS_VDW
public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms)
calculateAsas()
or getGroupAsas()
to calculate the ASAs
Only non-Hydrogen atoms are considered in the calculation.structure
- probe
- nSpherePoints
- nThreads
- hetAtoms
- if true HET residues are considered, if false they aren't, equivalent to
NACCESS' -h optionStructureTools.getAllNonHAtomArray
public AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads)
calculateAsas()
or getGroupAsas()
to calculate the ASAs.atoms
- an array of atoms not containing Hydrogen atomsprobe
- the probe sizenSpherePoints
- the number of points to be used in generating the spherical
dot-density, the more points the more accurate (and slower) calculationnThreads
- the number of parallel threads to use for the calculationIllegalArgumentException
- if any atom in the array is a Hydrogen atompublic GroupAsa[] getGroupAsas()
ResidueNumber
public double[] calculateAsas()
public static double getRadius(Atom atom)
#Element().N
is returnedatom
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